Comprehensive multi-omics analysis uncovers potential risks of aged sperm on offspring development after short-term storage by Yu Cheng, Songpei Zhang, Sayyed Mohammad Hadi Alavi, Rigolin Nayak, Swapnil Gorakh Waghmare, Nururshopa Eskander Shazada, Deepali Rahi Roy, Zhijun Ma, Otomar Linhart, Zuzana Linhartová

“…We combined DNA methylome, transcriptomic and proteomic data to elucidate the potential mechanisms by which sperm storage influences progeny development. …”
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Role of Methyl thiobutyrate to Botrytis cinerea on cucumber by Nv Chang, Rui Liu, Cuihua Lu, Yuqing Lai, Qian Xu, Yuhong Yang, Yan Li, Jian Ling, Bingyan Xie, Wenchao Zhao, Zhenchuan Mao, Jianlong Zhao

“…These results demonstrate the potential of MTB as an effective biocontrol agent against B. cinerea and provide valuable insights into its underlying mechanisms of action.…”
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p53-loss induced prostatic epithelial cell plasticity and invasion is driven by a crosstalk with the tumor microenvironment by Darya Yanushko, Beatriz German Falcon, Rana El Bizri, Despoina Pervizou, Robin Dolgos, Céline Keime, Tao Ye, Christelle Thibault-Carpentier, Clementine Le Magnen, Sandrine Henri, Gilles Laverny, Daniel Metzger

“…Moreover, we show that the transcriptomic signature of this cell population is prominent in tumors of patients with high-risk prostate cancer or metastatic disease. …”
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Transcription factor 3 is dysregulated in megakaryocytes in myelofibrosis by Ryan J Collinson, Lynne Wilson, Darren Boey, Zi Yun Ng, Bob Mirzai, Hun S Chuah, Rebecca Howman, Carolyn S Grove, Jacques A J Malherbe, Michael F Leahy, Matthew D Linden, Kathryn A Fuller, Wendy N Erber, Belinda B Guo

“…We then progressed to transcriptomic sequencing of platelets which showed loss of TCF3 in MF. …”
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Longitudinal MRI‐Driven Multi‐Modality Approach for Predicting Pathological Complete Response and B Cell Infiltration in Breast Cancer by Yu‐Hong Huang, Zhen‐Yi Shi, Teng Zhu, Tian‐Han Zhou, Yi Li, Wei Li, Han Qiu, Si‐Qi Wang, Li‐Fang He, Zhi‐Yong Wu, Ying Lin, Qian Wang, Wen‐Chao Gu, Chang‐Cong Gu, Xin‐Yang Song, Yang Zhou, Dao‐Gang Guan, Kun Wang

“…In clinical practice, this study provides a noninvasive tool to accurately predict pCR, with the potential to guide treatment planning and improve breast‐conserving surgery rates. …”
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High levels of histone acetylation modifications promote the formation of PGCs by Ziduo Zhao, Yuhui Wu, Fufu Cheng, Zhe Wang, Qingqing Geng, Yingjie Niu, Qisheng Zuo, Yani Zhang

“…This study investigates the role of histone acetylation in the differentiation of chicken embryonic stem cells (ESCs) into primordial germ cells (PGCs). Transcriptomic sequencing was used to analyze differentially expressed genes during this differentiation process, with functional annotation identifying genes associated with histone acetylation. …”
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PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy by Paul Nghiem, Martin Cheever, Stanley R Riddell, Steven P Fling, Nirasha Ramchurren, Nathalie Labarrière, Sylvain Simon, Virginie Vignard, Tiffany Beauvais, Brigitte Dreno, Valentin Voillet, Zhong Wu, Camille Dabrowski, Nicolas Jouand, Amir Khammari, Cécile Braudeau, Régis Josien, Olivier Adotevi, Caroline Laheurte, François Aubin, Charles Nardin, Samuel Rulli, Raphael Gottardo, Candice D Church

“…This DPOS T-cell population was enriched in highly activated T-cells, tumor-specific and emerging T-cell clonotypes and T lymphocytes overexpressing CXCR5, a key marker of the CD8 cytotoxic follicular T cell population. Additionally, transcriptomic profiling defined a specific gene signature for this population as well as the overexpression of specific pathways associated with the therapeutic response.Conclusions Our results provide a convincing rationale for monitoring this PD-1+TIGIT+ circulating population as an early cellular-based marker of therapeutic response to anti-PD-1 therapy.…”
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Deciphering the role of IL17RA in psoriasis and chronic mucocutaneous candidiasis: shared pathways and distinct manifestations by Ayat Kadhi, Ayat Kadhi, Ayat Kadhi, Edward Eid, Michel J. Massaad, Inaam El-Rassy, Dana Maria Khoury, Yutaka Shimomura, Nelly Rubeiz, Mazen Kurban, Mazen Kurban, Mazen Kurban, Georges Nemer, Georges Nemer

“…Our findings bridge a critical knowledge gap and provide insights into the molecular mechanisms connecting these diseases. …”
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Comprehensive molecular portrait reveals genetic diversity and distinct molecular subtypes of small intestinal neuroendocrine tumors by Céline Patte, Roxane M. Pommier, Anthony Ferrari, Felicia Fei-Lei Chung, Maria Ouzounova, Pauline Moullé, Mathieu Richaud, Rita Khoueiry, Maëva Hervieu, Silvia Breusa, Marion Allio, Nicolas Rama, Laura Gérard, Valérie Hervieu, Gilles Poncet, Tanguy Fenouil, Vincent Cahais, Anne-Sophie Sertier, Anne Boland, Delphine Bacq-Daian, Benjamin Ducarouge, Julien C. Marie, Jean-François Deleuze, Alain Viari, Jean-Yves Scoazec, Colette Roche, Patrick Mehlen, Thomas Walter, Benjamin Gibert

“…Here, by performing a multi-omics analysis of siNETs, we unveil four distinct molecular groups with strong clinical relevance and provide a resource to study their origin and clinical features. …”
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Epigenetic determinants of an immune-evasive phenotype in HER2-low triple-negative breast cancer by Andrés F. Bedoya-López, Sookyung Ahn, Miquel Ensenyat-Mendez, Javier I. J. Orozco, Sandra Iñiguez-Muñoz, Pere Llinàs-Arias, Samantha M. Thomas, Jennifer L. Baker, Peggy S. Sullivan, Jitin Makker, Julie B. Steele, Sunil M. Kurian, Diego M. Marzese, Maggie L. DiNome

“…We performed a comprehensive multi-omics analysis, integrating genomic, epigenomic, transcriptomic, and proteomic profiling to characterize HER2-low TNBC. …”
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Gene mapping and identification of candidate genes controlling carotenoid accumulation of yellow kernels in foxtail millet by Junjie Wang, Qi Ma, Yuyang Zhang, Qian Duan, Xiaoxi Zhen, Yaoyuan Zhang, Hongying Li, Yuanhuai Han, Bin Zhang

“…Conclusions These findings provide crucial genetic insights for the molecular mechanisms involved in carotenoid metabolism and lay a solid foundation for millet color breeding in foxtail millet.…”
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Formononetin Exerts Neuroprotection in Parkinson’s Disease via the Activation of the Nrf2 Signaling Pathway by Xiaotong Wang, Nianxin Kang, Ying Liu, Guojie Xu

“…The signaling pathway induced by FMN was analyzed using transcriptomic techniques and subsequently validated in vitro. …”
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Wild-type bone marrow cells repopulate tissue resident macrophages and reverse the impacts of homozygous CSF1R mutation. by Dylan Carter-Cusack, Stephen Huang, Sahar Keshvari, Omkar Patkar, Anuj Sehgal, Rachel Allavena, Robert A J Byrne, B Paul Morgan, Stephen J Bush, Kim M Summers, Katharine M Irvine, David A Hume

“…The transcriptomic profiles revealed subtle effects of macrophage deficiency on development of all major organs. …”
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Blood–brain barrier disruption and neuroinflammation in the hippocampus of a cardiac arrest porcine model: Single-cell RNA sequencing analysis by Tangxing Jiang, Yaning Li, Hehui Liu, Yijun Sun, Huidan Zhang, Qirui Zhang, Shuyao Tang, Xu Niu, Han Du, Yinxia Yu, Hongwei Yue, Yunyun Guo, Yuguo Chen, Feng Xu

“…In this study, we performed a single-cell transcriptomic analysis of the hippocampus from pigs with ventricular fibrillation-induced cardiac arrest at 6 and 24 hours following the return of spontaneous circulation, and from sham control pigs. …”
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Identification of the Different Gene Expression Characteristics from Liver Cirrhosis to Hepatocellular Carcinoma Using Single-Cell Sequencing Analyses by Xin Xing, Jian Song

“…We found that eight genes that are specifically expressed in the endothelial cell and stellate cell of the HCC patients and correlated them with their survival rate, which may provide novel diagnosis and treatment targets for the clinical application.…”
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TREM2 in MASH: integrating lipid metabolism and immune response by Shuyi Shi, Yangyang Zhou, Haiming Zhang, Junli Zhang

“…Several studies have demonstrated that TREM2+ macrophages play a crucial role in lipid metabolism and immune responses, contributing to the reversal of MASH. This review provides a comprehensive overview of the current evidence on the roles of TREM2+macrophages in regulating lipid metabolism and immune responses in MASH, with emphasis on the functions of TREM2+ macrophages in lipid handling and inflammation regulation, which could provide novel insights into the pathogenesis of MASH and inform targeted therapeutic strategies.…”
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Impact of c-di-AMP Accumulation, L-cysteine, and Oxygen on Catalase Activity and Oxidative Stress Resistance of <i>Listeria monocytogenes</i> 10403S by Mahide Muge Yilmaz Topcam, Dimitrios P. Balagiannis, Kimon Andreas G. Karatzas

“…Our transcriptomic data provided promising insights into the molecular mechanisms underlying c-di-AMP regulation, which may enhance stress resistance. …”
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The glycosaminoglycan chains of perlecan regulate the perivascular fluid transport by Abhishek Singh, Mika Kaakinen, Harri Elamaa, Vesa Kiviniemi, Lauri Eklund

“…Potentially deleterious effects on brain homeostasis were investigated using transcriptomic, proteomic and immunohistochemical methods. …”
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Single-cell and spatial analyses of the GDF family in tumors, with a focus on the prognostic and biological role of GDF15 in hepatocellular carcinoma by Xiaoqian Feng, Qian Huai, Fumin Zhang, Wenkang Yuan, Xingyu Li, Zhuo Yu, Hao Zhang, Yaoling Zhu, Xu Zhang, Baole Tao, Ying Dai, Yishan Du

“…Notably, validation analyses in bulk RNA-seq consistently emphasized the clinical significance of these findings. This study provides a comprehensive overview of the oncogenic role of the GDF subfamily in a wide range of tumors, highlights the important role of GDF15 in HCC ecosystem, and provides important biomarkers and potential therapeutic targets for future research.…”
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CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning by Jiaxing Bai, Yichun Gao, Feng Zhou, Yushuang He, Chen Lin, Xiaobing Huang, Ying Wang

“…It also excels in spatial transcriptomics by accurately identifying cancer spots. …”
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